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NEWS
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NEWS
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## 0.1.1
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- EUCAST_rules applies for amoxicillin even if ampicillin is missing
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- Edited column names to comply with GLIMS, the laboratory information system
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## 0.1.0
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- First submission to CRAN.
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69
R/EUCAST.R
69
R/EUCAST.R
@ -37,11 +37,19 @@
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#' EUCAST Expert Rules Version 3.1: \cr
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#' \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
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#' @examples
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#' \dontrun{
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#' tbl <- EUCAST_rules(tbl)
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#' }
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#' a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
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#' vanc = "-",
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#' amox = "-",
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#' coli = "-",
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#' cfta = "-",
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#' cfur = "-",
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#' stringsAsFactors = FALSE)
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#' a
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#'
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#' b <- EUCAST_rules(a)
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#' b
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EUCAST_rules <- function(tbl,
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col_bactcode = 'bacteriecode',
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col_bactcode = 'bactid',
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info = TRUE,
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amcl = 'amcl',
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amik = 'amik',
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@ -232,61 +240,61 @@ EUCAST_rules <- function(tbl,
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# Citrobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
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cols = c(ampi, tica))
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cols = c(aminopenicillines, tica))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
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cols = c(ampi, amcl, czol, cfox))
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cols = c(aminopenicillines, amcl, czol, cfox))
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# Enterobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
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cols = c(ampi, amcl, czol, cfox))
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cols = c(aminopenicillines, amcl, czol, cfox))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
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cols = c(ampi, amcl, czol, cfox))
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cols = c(aminopenicillines, amcl, czol, cfox))
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# Escherichia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Escherichia hermanni'),
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cols = c(ampi, tica))
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cols = c(aminopenicillines, tica))
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# Hafnia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Hafnia alvei'),
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cols = c(ampi, amcl, czol, cfox))
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cols = c(aminopenicillines, amcl, czol, cfox))
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# Klebsiella
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Klebsiella'),
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cols = c(ampi, tica))
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cols = c(aminopenicillines, tica))
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# Morganella / Proteus
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Morganella morganii'),
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cols = c(ampi, amcl, czol, tetracyclines, polymyxines, nitr))
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cols = c(aminopenicillines, amcl, czol, tetracyclines, polymyxines, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Proteus mirabilis'),
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cols = c(tetracyclines, tige, polymyxines, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Proteus penneri'),
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cols = c(ampi, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Proteus vulgaris'),
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cols = c(ampi, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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# Providencia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Providencia rettgeri'),
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cols = c(ampi, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Providencia stuartii'),
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cols = c(ampi, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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# Raoultella
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Raoultella'),
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cols = c(ampi, tica))
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cols = c(aminopenicillines, tica))
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# Serratia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Serratia marcescens'),
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cols = c(ampi, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxines, nitr))
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cols = c(aminopenicillines, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxines, nitr))
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# Yersinia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
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cols = c(ampi, amcl, tica, czol, cfox))
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cols = c(aminopenicillines, amcl, tica, czol, cfox))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
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cols = c(poly, coli))
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@ -313,32 +321,32 @@ EUCAST_rules <- function(tbl,
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# Acinetobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'),
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cols = c(ampi, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
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cols = c(aminopenicillines, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
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# Achromobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
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cols = c(ampi, czol, cfot, cftr, erta))
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cols = c(aminopenicillines, czol, cfot, cftr, erta))
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# Burkholderia
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edit_rsi(to = 'R',
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# onder 'Burkholderia cepacia complex' vallen deze species allemaal: PMID 16217180.
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rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
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cols = c(ampi, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosiden, trim, fosf, polymyxines))
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cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosiden, trim, fosf, polymyxines))
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# Elizabethkingia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'),
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cols = c(ampi, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxines))
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cols = c(aminopenicillines, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxines))
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# Ochrobactrum
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
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cols = c(ampi, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
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cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
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# Pseudomonas
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
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cols = c(ampi, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
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cols = c(aminopenicillines, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
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# Stenotrophomonas
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
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cols = c(ampi, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosiden, trim, fosf, tetr))
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cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosiden, trim, fosf, tetr))
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# Table 3: Intrinsic resistance in other Gram-negative bacteria ----
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@ -448,6 +456,12 @@ EUCAST_rules <- function(tbl,
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& tbl[, ampi] == 'R'),
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cols = c(ureidopenicillines, carbapenems))
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}
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if (!is.na(amox)) {
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edit_rsi(to = 'R',
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rows = which(tbl$genus == 'Enterococcus'
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& tbl[, amox] == 'R'),
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cols = c(ureidopenicillines, carbapenems))
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}
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# Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
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if (info == TRUE) {
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@ -579,7 +593,7 @@ EUCAST_rules <- function(tbl,
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cols = trim)
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}
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if (!is.na(ampi) & !is.na(amox)) {
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tbl[, amox] <- tbl[, ampi]
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tbl[, amox] <- tbl %>% pull(ampi)
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}
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# Toegevoegde kolommen weer verwijderen
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@ -596,6 +610,7 @@ EUCAST_rules <- function(tbl,
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tbl
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}
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#' @name EUCAST
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#' @rdname EUCAST
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#' @export
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interpretive_reading <- function(...) {
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53
README.md
53
README.md
@ -40,14 +40,37 @@ library(AMR)
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# For a list of functions:
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help(package = "AMR")
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```
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### Databases included in package
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### Overwrite/force resistance based on EUCAST rules
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This is also called *interpretive reading*.
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```r
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# Dataset with ATC antibiotics codes, official names and DDD's (oral and parenteral)
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ablist # A tibble: 420 x 12
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before <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
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"ENCFAE" # Enterococcus faecalis
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"ESCCOL", # Escherichia coli
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"KLEPNE", # Klebsiella pneumoniae
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"PSEAER"), # Pseudomonas aeruginosa
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vanc = "-", # Vancomycin
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amox = "-", # Amoxicillin
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coli = "-", # Colistin
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cfta = "-", # Ceftazidime
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cfur = "-", # Cefuroxime
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stringsAsFactors = FALSE)
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before
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# bactid vanc amox coli cfta cfur
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# 1 STAAUR - - - - -
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# 2 ENCFAE - - - - -
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# 3 ESCCOL - - - - -
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# 4 KLEPNE - - - - -
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# 5 PSEAER - - - - -
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# Dataset with bacteria codes and properties like gram stain and aerobic/anaerobic
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bactlist # A tibble: 2,507 x 10
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# Now apply those rules; just need a column with bacteria ID's and antibiotic results:
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after <- EUCAST_rules(before)
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after
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# bactid vanc amox coli cfta cfur
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# 1 STAAUR - - R R -
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# 2 ENCFAE - - R R R
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# 3 ESCCOL R - - - -
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# 4 KLEPNE R R - - -
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# 5 PSEAER R R - - R
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```
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### New classes
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@ -94,18 +117,13 @@ plot(rsi_data)
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Other epidemiological functions:
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```r
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# Apply EUCAST Expert Rules v3.1 (latest) to antibiotic columns
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EUCAST_rules(...)
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# Determine key antibiotic based on bacteria ID
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key_antibiotics(...)
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# Check if key antibiotics are equal
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key_antibiotics_equal(...)
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# Selection of first isolates of any patient
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first_isolate(...)
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# Calculate resistance levels of antibiotics
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# Calculate resistance levels of antibiotics, can be used with `summarise` (dplyr)
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rsi(...)
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# Predict resistance levels of antibiotics
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rsi_predict(...)
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@ -115,6 +133,17 @@ abname(...)
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abname("J01CR02", from = "atc", to = "umcg") # "AMCL"
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```
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### Databases included in package
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Datasets to work with antibiotics and bacteria properties.
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```r
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# Dataset with ATC antibiotics codes, official names and DDD's (oral and parenteral)
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ablist # A tibble: 420 x 12
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# Dataset with bacteria codes and properties like gram stain and aerobic/anaerobic
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bactlist # A tibble: 2,507 x 10
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```
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## Authors
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- [Berends MS](https://github.com/msberends)<sup>1,2</sup>, PhD Student
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@ -3,6 +3,7 @@
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\name{EUCAST}
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\alias{EUCAST}
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\alias{EUCAST_rules}
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\alias{EUCAST}
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\alias{interpretive_reading}
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\title{EUCAST expert rules}
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\source{
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@ -14,22 +15,22 @@ EUCAST Expert Rules Version 2.0: \cr
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\url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
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}
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\usage{
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EUCAST_rules(tbl, col_bactcode = "bacteriecode", info = TRUE,
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amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
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azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
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cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
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cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr",
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clar = "clar", clin = "clin", clox = "clox", coli = "coli",
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czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta",
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eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent",
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imip = "imip", kana = "kana", levo = "levo", linc = "linc",
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line = "line", mero = "mero", mino = "mino", moxi = "moxi",
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nali = "nali", neom = "neom", neti = "neti", nitr = "nitr",
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novo = "novo", norf = "norf", oflo = "oflo", peni = "peni",
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pita = "pita", poly = "poly", qida = "qida", rifa = "rifa",
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roxi = "roxi", siso = "siso", teic = "teic", tetr = "tetr",
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tica = "tica", tige = "tige", tobr = "tobr", trim = "trim",
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trsu = "trsu", vanc = "vanc")
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EUCAST_rules(tbl, col_bactcode = "bactid", info = TRUE, amcl = "amcl",
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amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
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aztr = "aztr", cefa = "cefa", cfra = "cfra", cfep = "cfep",
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cfot = "cfot", cfox = "cfox", cfta = "cfta", cftr = "cftr",
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cfur = "cfur", chlo = "chlo", cipr = "cipr", clar = "clar",
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clin = "clin", clox = "clox", coli = "coli", czol = "czol",
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dapt = "dapt", doxy = "doxy", erta = "erta", eryt = "eryt",
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fosf = "fosf", fusi = "fusi", gent = "gent", imip = "imip",
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kana = "kana", levo = "levo", linc = "linc", line = "line",
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mero = "mero", mino = "mino", moxi = "moxi", nali = "nali",
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neom = "neom", neti = "neti", nitr = "nitr", novo = "novo",
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norf = "norf", oflo = "oflo", peni = "peni", pita = "pita",
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poly = "poly", qida = "qida", rifa = "rifa", roxi = "roxi",
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siso = "siso", teic = "teic", tetr = "tetr", tica = "tica",
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tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu",
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vanc = "vanc")
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interpretive_reading(...)
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}
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@ -51,7 +52,15 @@ table with edited variables of antibiotics.
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Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
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}
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\examples{
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\dontrun{
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tbl <- EUCAST_rules(tbl)
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}
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a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
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vanc = "-",
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amox = "-",
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coli = "-",
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cfta = "-",
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cfur = "-",
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stringsAsFactors = FALSE)
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a
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b <- EUCAST_rules(a)
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b
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}
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